Merge pull request #1471 from ESMCI/erichlf/case_submit/skip_pnl

Add skip-preview-namelist to case.submit and case_run

Added '--skip-preview-namelist' to case.build

Added '--skip-preview-namelist' to case.build. This will allow the user
to specify if the namelist should be rebuilt from user_nl_*.

Test suite: scripts_regression_tests.py
Test baseline:
Test namelist changes:
Test status: bit for bit

Fixes #1276, E3SM-Project/E3SM#1466

User interface changes?: Added --skip-preview-namelist to case.build and
template.case.run

Code review: @jgfouca, @rljacob, @jedwards4b

config/cesm/machines/template.case.run

@@ -29,35 +29,37 @@ import argparse, doctest
 def parse_command_line(args, description):
 ###############################################################################
     parser = argparse.ArgumentParser(
-        usage="""\n%s [--verbose]
+        usage="""\n{0} [--verbose]
 OR
-%s --help
+{0} --help
 OR
-%s --test
+{0} --test
 
 \033[1mEXAMPLES:\033[0m
     \033[1;32m# case.run SMS\033[0m
-    > %s
-""" % ((os.path.basename(args[0]), ) * 4),
-
-description=description,
-
-formatter_class=argparse.ArgumentDefaultsHelpFormatter
-)
-
-    parser = argparse.ArgumentParser()
+    > {0}
+""".format(os.path.basename(args[0])),
+        description=description,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
 
     CIME.utils.setup_standard_logging_options(parser)
 
     parser.add_argument("--caseroot",
                         help="Case directory to build")
 
+    parser.add_argument("--skip-preview-namelist", action="store_true",
+                        help="Skip calling preview-namelist during case.run")
+
     args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
 
-    return args.caseroot
+    if args.skip_preview_namelist is None:
+        args.skip_preview_namelist = False
+
+    return args.caseroot, args.skip_preview_namelist
 
 ###############################################################################
 def _main_func(description):
@@ -66,9 +68,9 @@ def _main_func(description):
         test_results = doctest.testmod(verbose=True)
         sys.exit(1 if test_results.failed > 0 else 0)
 
-    caseroot = parse_command_line(sys.argv, description)
+    caseroot, skip_pnl = parse_command_line(sys.argv, description)
     with Case(caseroot, read_only=False) as case:
-        success = case_run(case)
+        success = case_run(case, skip_pnl=skip_pnl)
 
     sys.exit(0 if success else 1)